Ma. del Socorro Gama Castro
Telephone: (777) 3132063
Email: sgama@ccg.unam.mx
Publications
| Year | Publication | PMID |
|---|---|---|
| 2019 | Santos-Zavaleta, A, Salgado, H, Gama-Castro, S, Sánchez-Pérez, M, Gómez-Romero, L, Ledezma-Tejeida, D, García-Sotelo, J, Alquicira-Hernández, K, Muñiz-Rascado, L, Peña-Loredo, P, Ishida-Gutiérrez, C, Velázquez-Ramírez, D, Del Moral-Chávez, V, Bonavides-Martínez, C, Méndez-Cruz, C, Galagan, J, Collado-Vides, J. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077] | 30395280 |
| 2019 | Tierrafría, V, Mejía-Almonte, C, Camacho-Zaragoza, J, Salgado, H, Alquicira, K, Ishida, C, Gama-Castro, S, Collado-Vides, J. (2019). "MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.". Bioinformatics. 35(5):856-864. [doi:10.1093/bioinformatics/bty689] | 30137210 |
| 2017 | Méndez-Cruz CF, Gama-Castro S, Mejía-Almonte C, Castillo-Villalba MP, Muñiz-Rascado LJ, Collado-Vides J. (2017). "First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017():bax070-. [doi:10.1093/database/bax070] | 29220462 |
| 2017 | Keseler, I, Mackie, A, Santos-Zavaleta, A, Billington, R, Bonavides-Martínez, C, Caspi, R, Fulcher, C, Gama-Castro, S, Kothari, A, Krummenacker, M, Latendresse, M, Muñiz-Rascado, L, Ong, Q, Paley, S, Peralta-Gil, M, Subhraveti, P, Velázquez-Ramírez, D, Weaver, D, Collado-Vides, J, Paulsen, I, Karp, P. (2017). "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.". Nucleic Acids Research. 45(D1):543-550. [doi:10.1093/nar/gkw1003] | 27899573 |
| 2016 | Moretto, M, Sonego, P, Dierckxsens, N, Brilli, M, Bianco, L, Ledezma-Tejeida, D, Gama-Castro, S, Galardini, M, Romualdi, C, Laukens, K, Collado-Vides, J, Meysman, P, Engelen, K. (2016). "COLOMBOS v3.0: Leveraging gene expression compendia for cross-species analyses". Nucleic Acids Research. 44(D1):620-623. [doi:10.1093/nar/gkv1251] | 26586805 |
| 2016 | Gama-Castro, S, Salgado, H, Santos-Zavaleta, A, Ledezma-Tejeida, D, Muñiz-Rascado, L, García-Sotelo, J, Alquicira-Hernández, K, Martínez-Flores, I, Pannier, L, Castro-Mondragón, J, Medina-Rivera, A, Solano-Lira, H, Bonavides-Martínez, C, Pérez-Rueda, E, Alquicira-Hernández, S, Porrón-Sotelo, L, López-Fuentes, A, Hernández-Koutoucheva, A, Del Moral-Chavez, V, Rinaldi, F, Collado-Vides, J. (2016). "RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering and beyond". Nucleic Acids Research. 44(D1):133-143. [doi:10.1093/nar/gkv1156] | 26527724 |
| 2016 | Wang, Q, Abdul, S, Almeida, L, Ananiadou, S, Balderas-Martinez, Y, Batista-Navarro, R, Campos, D, Chilton, L, Chou, H, Contreras, G, Cooper, L, Dai, H, Ferrell, B, Fluck, J, Gama-Castro, S, George, N, Gkoutos, G, Irin, A, Jensen, L, Jimenez, S, Jue, T, Keseler, I, Madan, S, Matos, S, McQuilton, P, Milacic, M, Mort, M, Natarajan, J, Pafilis, E, Pereira, E, Rao, S, Rinaldi, F, Rothfels, K, Salgado, D, Silva, R, Singh, O, Stefancsik, R, Su, C, Subramani, S, Tadepally, H, Tsaprouni, L, Vasilevsky, N, Wang, X, Chatr-Aryamontri, A, Laulederkind, S, Matis-Mitchell, S, McEntyre, J, Orchard, S, Pundir, S, Rodriguez-Esteban, R, Van Auken, K, Lu, Z, Schaeffer, M, Wu, C, Hirschman, L, Arighi, C. (2016). "Overview of the interactive task in BioCreative V". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2016():baw119-. [doi:10.1093/database/baw119] | 27589961 |
| 2014 | Gama Castro, M, Rinaldi, F, López Fuentes, A, Balderas MartÍnez, Y, Clematide, S, Ellendorff, T, Santos Zavaleta, A, Marques-Madeira, H, Collado Vides, P. (2014). "Assisted curation of regulatory interactions and growth conditions of OxyR in E. Colik-12". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2014():bau049-. [doi:10.1093/database/bau049] | 24903516 |
| 2014 | Meysman, P, Sonego, P, Bianco, L, Fu, Q, Ledezma Tejeida, D, Gama Castro, M, Liebens, V, Laukens, K, Marchal, K, Collado Vides, P, Engelen, K. (2014). "COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia". Nucleic Acids Research. 42(D1):649-653. [doi:10.1093/nar/gkt1086] | 24214998 |
| 2013 | Salgado Osorio, H, Peralta Gil, M, Gama Castro, M, Santos Zavaleta, A, Muñíz Rascado, L, Garcia Sotelo, J, Weiss, V, Solano Lira, H, Martínez Flores, I, Medina Rivera, A, Salgado Osorio, G, Alquicira Hernández, S, Alquicira Hernández, K, López Fuentes, A, Porrón Sotelo, L, Huerta Moreno, A, Bonavides Martínez, C, Balderas MartÍnez, Y, Pannier, L, Olvera, M, Labastida, A, Jiménez-Jacinto, V, Vega-Alvarado, L, del Moral Chávez, V, Hernández Álvarez, A, Morett, E, Collado Vides, P. (2013). "RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more". Nucleic Acids Research. 41(D1):203-213. [doi:10.1093/nar/gks1201] | 23203884 |
| 2013 | Keseler, I, Mackie, A, Peralta Gil, M, Santos Zavaleta, A, Gama Castro, M, Bonavides Martínez, C, Fulcher, C, Huerta Moreno, A, Kothari, A, Krummenacker, M, Latendresse, M, Muñíz Rascado, L, Ong, Q, Paley, S, Schroder, I, Shearer, A, Subhraveti, P, Travers, M, Weerasinghe, D, Weiss, V, Collado Vides, P, Gunsalus, R, Paulsen, I, Karp, P. (2013). "EcoCyc: Fusing model organism databases with systems biology". Nucleic Acids Research. 41(D1):605-612. [doi:10.1093/nar/gks1027] | 23143106 |
| 2011 | Santos Zavaleta, A, Gama Castro, M, Pérez Rueda, E. (2011). "A comparative genome analysis of the RpoS sigmulon shows a high diversity of responses and origins". MICROBIOLOGY-UK. 157(5):1393-1401. [doi:10.1099/mic.0.042937-0] | 21310789 |
| 2011 | Keseler, I, Collado Vides, P, Santos Zavaleta, A, Peralta Gil, M, Gama Castro, M, Muñíz Rascado, L, Bonavides Martínez, C, Paley, S, Krummenacker, M, Altman, T, Spaulding, A, Spaulding, A, Pacheco, J, Latendresse, M, Fulcher, C, Sarker, M, Shearer, A, Mackie, A, Paulsen, I, Gunsalus, R, Karp, P. (2011). "EcoCyc: A comprehensive database of Escherichia coli biology". Nucleic Acids Research. 39(SUPPL. 1):583-590. [doi:10.1093/nar/gkq1143] | 21097882 |
| 2011 | Gama Castro, M, Salgado Osorio, H, Peralta Gil, M, Santos Zavaleta, A, Muñíz Rascado, L, Solano Lira, H, Jimenez-Jacinto, V, Weiss, V, Garcia Sotelo, J, López Fuentes, A, Porrón Sotelo, L, Alquicira Hernández, S, Medina Rivera, A, Martínez Flores, I, Alquicira Hernández, K, Martínez Adame, R, Bonavides Martínez, C, Miranda-Ríos, J, Huerta Moreno, A, Mendoza-Vargas, A, Collado Torres, L, Taboada, B, Vega-Alvarado, L, Olvera, M, Olvera, L, Grande, R, Morett, E, Collado Vides, P. (2011). "RegulonDB version 7.0: Transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)". Nucleic Acids Research. 39(SUPPL. 1):98-105. [doi:10.1093/nar/gkq1110] | 21051347 |
| 2009 | Collado-Vides, J, Salgado, H, Morett, E, Gama-Castro, S, Jimenez-Jacinto, V, Martinez-Flores, I, Medina-Rivera, A, Muniz-Rascado, L, Peralta-Gil, M, Santos-Zavaleta, A. (2009). "Bioinformatics resources for the study of gene regulation in bacteria". Journal Of Bacteriology. 91(1):23-31. [doi:10.1128/JB.01017-08] | 18978060 |
| 2008 | Gama Castro, M, Jiménez Jacinto, V, Peralta Gil, M, Santos Zavaleta, A, Peñaloza Spinola, M, Contreras Moreira, B, Segura Salazar, J, Muñíz Rascado, L, Martínez Flores, I, Salgado Osorio, H, Bonavides Martínez, C, Abreu Goodger, C, Rodríguez Penagos, C, Miranda-Ríos, J, Morett Sánchez, J, Merino, E, Huerta Moreno, A, Treviño Quintanilla, L, Collado Vides, P. (2008). "RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation". Nucleic Acids Research. 36(SUPPL. 1):120-124. [doi:10.1093/nar/gkm994] | 18158297 |
| 2007 | Karp, P, Keseler, I, Shearer, A, Latendresse, M, Krummenacker, M, Paley, S, Paulsen, I, Collado Vides, P, Gama Castro, M, Peralta Gil, M, Santos Zavaleta, A, Peñaloza Spinola, M, Bonavides Martínez, C, Ingraham, J. (2007). "Multidimensional annotation of the Escherichia coli K-12 genome". Nucleic Acids Research. 35(22):7577-7590. [doi:10.1093/nar/gkm740] | 17940092 |
| 2006 | Salgado Osorio, H, Santos Zavaleta, A, Gama Castro, M, Peralta Gil, M, Peñaloza Spinola, M, Martínez Antonio, A, Karp, P, Collado Vides, P. (2006). "The comprehensive updated regulatory network of Escherichia coli K-12". Bmc Bioinformatics. 7():5-5. [doi:10.1186/1471-2105-7-5] | 16398937 |
| 2006 | Salgado Osorio, H, Gama Castro, M, Peralta Gil, M, Díaz Peredo, E, Sánchez Solano, E, Santos Zavaleta, A, Martínez Flores, I, Jiménez Jacinto, V, Bonavides Martínez, C, Segura Salazar, J, Martínez Antonio, A, Collado Vides, P. (2006). "RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.". Nucleic Acids Research. 34(Database issue):394-397. [doi:10.1093/nar/gkj156] | 16381895 |
| 2006 | Santos-Zavaleta, A, Salgado, H, Gama-Castro, S, Peralta-Gil, M, Contreras-Moreira, B, Penaloza-Spinola, M, Collado-Vides, J. (2006). "RegulonDB. The most important database in transcriptional regulatory network, operon organization, and growth conditions of Escherichia coli K12". Proceedings Of The Fifth International Conference On Bioinformatics Of Genome Regulation And Structure, Vol 3. ():323-323. | |
| 2005 | Keseler, I, Collado Vides, P, Gama Castro, M, Ingraham, J, Paley, S, Paulsen, I, Peralta Gil, M, Karp, P. (2005). "EcoCyc: A comprehensive database resource for Escherichia coli". Nucleic Acids Research. 33(DATABASE ISS.):334-337. [doi:10.1093/nar/gki108] | 15608210 |
| 2004 | Salgado Osorio, H, Gama Castro, M, Martínez Antonio, A, Díaz Peredo, E, Sánchez Solano, E, Peralta Gil, M, García Alonso, D, Jiménez Jacinto, V, Santos Zavaleta, A, Bonavides Martínez, C, Collado Vides, P. (2004). "RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12". Nucleic Acids Research. 32(DATABASE ISS.):303-306. [doi:10.1093/nar/gkh140] | 14681419 |
| 2002 | Collado Vides, P, Moreno Hagelsieb, G, Pérez Rueda, E, Salgado Osorio, H, Huerta Moreno, A, Gutiérrez Ríos, R, Rosenblueth, D, Christen, A, Benítez Bellón, E, Medrano Soto, L, Gama Castro, M, Santos Zavaleta, A, Bonavides Martínez, C, DíPeredo, E, Sánchez Solano, E, Millá, D. (2002). "Genomics of Gene Regulation: The view from Escherichia coli". Gene Regulation and Metabolism, Post-Genomic Computational Approaches. ():103-128. | |
| 2002 | Karp, P, Riley, M, Saier, M, Paulsen, I, Collado-Vides, J, Paley, S, Pellegrini-Toole, A, Bonavides, C, Gama-Castro, S. (2002). "The EcoCyc database". Nucleic Acids Research. 30(1):56-58. [doi:10.1093/nar/30.1.56] | 11752253 |
| 2001 | Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millen-Zarate, D, Diaz-Peredo, E, Sanchez-Solano, F, Pérez-Rueda, E, Bonavides-Martinez, C, Collado-Vides, J. (2001). "RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 29(1):72-74. [doi:10.1093/nar/29.1.72] | 11125053 |
| 2000 | Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millan-Zarate, D, Blattner, F, Collado-Vides, J. (2000). "RegulonDB (version 3.0): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 28(1):65-67. [doi:10.1093/nar/28.1.65] | 10592182 |
| 2003 | Martínez Antonio, A, Salgado Osorio, H, Gama Castro, M, Gutiérrez Ríos, R, Jiménez Jacinto, V, Collado Vides, P. (2003). "Environmental Conditions and Transcriptional Regulation in Escherichia coli: A Physiological Integrative Approach". BIOTECHNOLOGY AND BIOENGINEERING. 84(7):743-749. [doi:10.1002/bit.10846] | 14708114 |
| 2006 | Peñaloza Spinola, M, Peralta Gil, M, Gama Castro, M, Contreras Moreira, B, Santos Zavaleta, A, Martínez Flores, I, Collado Vides, P. (2006). "RegulonDB: Going beyond transcriptional regulation". Proceedings Of The Fifth International Conference On Bioinformatics Of Genome Regulation And Structure, Vol 3. ():322-322. | |
| 2017 | Rinaldi F, Lithgow O, Gama-Castro S, Solano H, Lopez A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J. (2017). "Strategies towards digital and semi-automated curation in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017(1):bax012-. [doi:10.1093/database/bax012] | 28365731 |
| 2018 | Santos-Zavaleta, A, Sanchez-Perez, M, Salgado, H, Velazquez-Ramirez, D, Gama-Castro, S, Tierrafria, V, Busby, S, Aquino, P, Fang, X, Palsson, B, Galagan, J, Collado-Vides, J. (2018). "A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0". BMC BIOLOGY. 16(1):91-91. [doi:10.1186/s12915-018-0555-y] | 30115066 |
| 2019 | Lithgow-Serrano, O, Gama-Castro, S, Ishida-Gutiérrez, C, Mejía-Almonte, C, Tierrafría, V, Martínez-Luna, S, Santos-Zavaleta, A, Velázquez-Ramírez, D, Collado-Vides, J. (2019). "Similarity corpus on microbial transcriptional regulation.". JOURNAL OF BIOMEDICAL SEMANTICS. 10(1):8-. [doi:10.1186/s13326-019-0200-x] | 31118102 |